meshmaker: Generating VTK PolyData from CCP4 Files

Please following the following steps to get meshmaker working.

Install CMake

If you have Homebrew installed:

brew install cmake

With Anaconda:

First ensure you have an environment available:

conda create -n meshmaker
conda activate meshmaker

then:

conda install cmake

Without Homebrew and Anaconda, download and install CMake from the CMake website.

Install VTK

With Homebrew:

brew install vtk

With Anaconda:

conda install vtk
conda install tbb tbb-devel

Without Homebrew or Anaconda, download and build from source.

Obtain source and prepare for build

Clone meshmaker and enter meshmaker directory:

user@mac ~ $ git clone https://github.com/emdb-empiar/meshmaker.git
Cloning into 'meshmaker'...
remote: Counting objects: 9, done.
remote: Compressing objects: 100% (9/9), done.
remote: Total 9 (delta 1), reused 5 (delta 0), pack-reused 0
Unpacking objects: 100% (9/9), done.
user@mac ~ $ cd meshmaker
user@mac ~ $ mkdir build
user@mac ~ $ cd build

Generate the Makefile

user@mac ~ $ cmake ..
-- The C compiler identification is AppleClang 8.1.0.8020042
-- The CXX compiler identification is AppleClang 8.1.0.8020042
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/pkorir/Downloads/meshmaker/build

Build

user@mac ~ $ make
Scanning dependencies of target meshmaker
[ 50%] Building CXX object CMakeFiles/meshmaker.dir/meshmaker.cpp.o
[100%] Linking CXX executable meshmaker.app/Contents/MacOS/meshmaker
[100%] Built target meshmaker

The executable for MacOSX is in the meshmaker.app/Contents/MacOS/ folder. You can use it directly like so:

    user@mac ~ $ meshmaker.app/Contents/MacOS/meshmaker -h
usage: meshmaker [options] file.map

Generate a mesh from the MAP/MRC file using the specified options

Options:
    -c/--clevel <float>
            the contour level at which to build the surface [default: 0.0]
    -o/--output <str>
            the prefix of the output file to be combined with the extension (see below) [default: out]
    -S/--stl        output in STL format
    -V/--vtk        output in VTK format
    -X/--vtp        output in VTP format [default]
    -D/--decimate   perform progressive decimation to eliminate superfluous polygons [default: false]
    -s/--smooth     smooth the generated surface [default: false]
    -i/--smooth-iter <int>
            number of iterations for smoothing (only applies if -s/--smooth is specified[default: 20]
    -t/--target-reduction <float>
            set the target reduction in the number of polygon in interval (0, 1) [default: 0.9]
    -A/--ascii      save data as ASCII as opposed to BINARY [default: false]
    -U/--uint64     save VTP headers using UInt64 as opposed to UInt32 [default: false]
    -I/--int32      use Int32 for vtkIdType instead of Int64 [default: false]
    -h/--help       show this help
    -v/--verbose    verbose output

Abort trap: 6

Optional: Install

make install

To specify a custom install prefix run

user@mac ~ $ ccmake ..

and modify the CMAKE_INSTALL_PREFIX variable.